[English] 日本語
Yorodumi
- PDB-8qjr: BRG1 bromodomain in complex with VBC via compound 17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qjr
TitleBRG1 bromodomain in complex with VBC via compound 17
Components
  • Elongin-B
  • Elongin-C
  • Transcription activator BRG1
  • von Hippel-Lindau disease tumor suppressor
KeywordsGENE REGULATION / BRG1 / BROMODOMAIN / VHL / ELONGIN / VBC / E3 LIGASE / VON HIPPEL-LINDAU / UBIQUITINASE
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / nBAF complex / regulation of cellular response to hypoxia / GBAF complex / neural retina development ...positive regulation of glucose mediated signaling pathway / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / nBAF complex / regulation of cellular response to hypoxia / GBAF complex / neural retina development / regulation of G0 to G1 transition / EGR2 and SOX10-mediated initiation of Schwann cell myelination / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / nucleosome disassembly / transcription elongation factor activity / regulation of nucleotide-excision repair / target-directed miRNA degradation / elongin complex / RSC-type complex / VCB complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / ATP-dependent chromatin remodeler activity / Replication of the SARS-CoV-1 genome / SWI/SNF complex / positive regulation of double-strand break repair / Cul5-RING ubiquitin ligase complex / positive regulation of T cell differentiation / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / nuclear androgen receptor binding / positive regulation of stem cell population maintenance / SUMOylation of ubiquitinylation proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of transcription elongation by RNA polymerase II / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / positive regulation of Wnt signaling pathway / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Formation of HIV elongation complex in the absence of HIV Tat / Chromatin modifying enzymes / negative regulation of signal transduction / DNA polymerase binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / transcription initiation-coupled chromatin remodeling / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / Interleukin-7 signaling / negative regulation of autophagy / helicase activity / transcription corepressor binding / transcription coregulator binding / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lysine-acetylated histone binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / positive regulation of DNA-binding transcription factor activity / nuclear matrix / positive regulation of miRNA transcription / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / nervous system development / Neddylation / positive regulation of cold-induced thermogenesis / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / amyloid fibril formation
Similarity search - Function
SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ ...SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Helicase/SANT-associated domain / HSA domain profile. / Elongin B / Elongin-C / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Ubiquitin family / Bromodomain / Ubiquitin homologues / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Ubiquitin domain profile. / helicase superfamily c-terminal domain / Ubiquitin-like domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Chem-VLH / von Hippel-Lindau disease tumor suppressor / Transcription activator BRG1 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsKerry, P.S. / Hole, A.J. / Perez-Dorado, J.I.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2024
Title: PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models.
Authors: Berlin, M. / Cantley, J. / Bookbinder, M. / Bortolon, E. / Broccatelli, F. / Cadelina, G. / Chan, E.W. / Chen, H. / Chen, X. / Cheng, Y. / Cheung, T.K. / Davenport, K. / DiNicola, D. / ...Authors: Berlin, M. / Cantley, J. / Bookbinder, M. / Bortolon, E. / Broccatelli, F. / Cadelina, G. / Chan, E.W. / Chen, H. / Chen, X. / Cheng, Y. / Cheung, T.K. / Davenport, K. / DiNicola, D. / Gordon, D. / Hamman, B.D. / Harbin, A. / Haskell, R. / He, M. / Hole, A.J. / Januario, T. / Kerry, P.S. / Koenig, S.G. / Li, L. / Merchant, M. / Perez-Dorado, I. / Pizzano, J. / Quinn, C. / Rose, C.M. / Rousseau, E. / Soto, L. / Staben, L.R. / Sun, H. / Tian, Q. / Wang, J. / Wang, W. / Ye, C.S. / Ye, X. / Zhang, P. / Zhou, Y. / Yauch, R. / Dragovich, P.S.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
G: Transcription activator BRG1
H: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,24019
Polymers111,3128
Non-polymers2,92911
Water1,02757
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
G: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29111
Polymers55,6564
Non-polymers1,6357
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
H: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9498
Polymers55,6564
Non-polymers1,2944
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.68, 88.044, 84.978
Angle α, β, γ (deg.)90, 105.89, 90
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 4 types, 8 molecules ADBECFGH

#1: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#3: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18702.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#4: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 14230.447 Da / Num. of mol.: 2 / Fragment: UNP residues 1418-1536
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

-
Non-polymers , 5 types, 68 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-VLH / (2S,4R)-1-[(2R)-2-[3-[2-[4-[3-[4-[(1R,5S)-3-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]pyridin-2-yl]oxycyclobutyl]oxypiperidin-1-yl]ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 1068.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C57H69N11O8S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 27 mM HEPES pH 6.8, 73 mM HEPES pH 8.6, 1.0 M NaI

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.17→80.64 Å / Num. obs: 20137 / % possible obs: 98.9 % / Redundancy: 3.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.3
Reflection shellResolution: 3.17→3.39 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2 / Num. unique obs: 3675 / CC1/2: 0.755 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→80.64 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.523
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 966 -RANDOM
Rwork0.262 ---
obs0.2628 20137 98.8 %-
Displacement parametersBiso mean: 67.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.4345 Å20 Å2-12.8328 Å2
2--2.7539 Å20 Å2
3----5.1884 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 3.17→80.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7290 0 196 57 7543
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0057656HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7510370HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2769SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1262HARMONIC5
X-RAY DIFFRACTIONt_it7656HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion976SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6033SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion16.17
LS refinement shellResolution: 3.17→3.19 Å
RfactorNum. reflection% reflection
Rfree0.374 16 -
Rwork0.3189 --
obs0.3207 420 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.43521.2377-1.04241.8365-0.7892.2724-0.0968-0.23790.1358-0.2379-0.11170.63810.13580.63810.2085-0.00320.02190.0699-0.05460.0657-0.194169.7562-7.961727.814
27.79951.7538-2.13575.8167-2.00293.0072-0.1392-0.35-0.3125-0.35-0.09620.1988-0.31250.19880.2355-0.14480.0477-0.0591-0.1928-0.0085-0.065953.7133-1.124222.9995
31.6744-0.38130.14711.9148-0.26351.5016-0.017-0.2705-0.0937-0.27050.022-0.09-0.0937-0.09-0.0050.0051-0.02490.0546-0.18830.0248-0.048133.3895-17.678813.2558
44.7880.229-3.40951.24340.09235.9226-0.0621-0.4941-0.0441-0.49410.0524-0.724-0.0441-0.7240.0098-0.109-0.0359-0.06030.0829-0.0861-0.164332.5078-3.3705-38.4375
56.2253-3.046-3.29017.82922.71124.9265-0.23710.03050.61950.0305-0.1908-0.39270.6195-0.39270.42790.0169-0.07080.0963-0.19080.0091-0.16528.6051-9.9265-22.0496
61.1925-0.10740.07063.19820.67433.08610.11290.29110.02780.2911-0.0878-0.38340.0278-0.3834-0.0252-0.0730.01180.0771-0.1380.0166-0.10126.13126.86970.3594
73.26260.0601-0.28175.086-1.14966.5887-0.21880.1578-0.22320.15780.1865-0.0102-0.2232-0.01020.0324-0.00840.1090.0458-0.3012-0.0763-0.077113.5842-56.02255.0354
811.11332.5306-0.23687.6354-1.68556.2088-0.2237-0.32590.2342-0.32590.9146-0.840.2342-0.84-0.69090.0983-0.13560.0036-0.15230.27750.033124.072644.450624.2194
9-0.1238-0.08570.19990.85530.04320.1238-0.0180.01760.00470.01760.0824-0.06210.0047-0.0621-0.0645-0.0408-0.01940.1029-0.35340.0172-0.085725.6193-5.40959.1501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|103 }A1 - 103
2X-RAY DIFFRACTION2{ B|16 - B|112 }B16 - 112
3X-RAY DIFFRACTION3{ C|61 - C|213 }C61 - 213
4X-RAY DIFFRACTION4{ D|1 - D|103 }D1 - 103
5X-RAY DIFFRACTION5{ E|16 - E|112 }E16 - 112
6X-RAY DIFFRACTION6{ F|60 - F|213 }F60 - 213
7X-RAY DIFFRACTION7{ G|1457 - G|1566 }G1457 - 1566
8X-RAY DIFFRACTION8{ H|1457 - H|1559 }H1457 - 1559
9X-RAY DIFFRACTION9{ C|305 - C|305 F|303 - F|303 }C305
10X-RAY DIFFRACTION9{ C|305 - C|305 F|303 - F|303 }F303

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more